Contacts of the strand formed by residues 260 - 269 (chain B) in PDB entry 3K8G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 260 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A HIS* 5.2 15.9 - - - -
215B GLU* 4.8 8.3 + - - -
230B SER* 2.9 38.1 + - - +
231B LEU 3.2 11.4 - - - +
232B GLN* 4.7 9.0 - - - +
233B LEU* 4.3 4.3 - - - -
256B VAL* 3.4 3.6 - - - +
257B GLU* 2.9 70.5 + - - +
258B GLY 3.4 1.4 + - - -
259B ASP* 1.3 89.0 - - - +
261B LEU* 1.3 60.6 + - - +
262B ILE* 3.4 18.2 + - + +
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Residues in contact with LEU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ILE* 5.3 2.7 - - + -
229B LEU* 3.8 2.3 - - - +
230B SER* 3.4 3.6 - - - -
231B LEU* 2.8 55.3 + - + +
233B LEU* 3.8 25.7 - - + +
238B ILE* 4.7 14.6 - - + -
243B GLN* 4.8 6.3 - - + -
246B ILE* 5.8 7.9 - - + -
254B ILE* 3.6 30.1 - - + -
255B HIS 3.8 5.8 - - - +
256B VAL* 4.3 13.2 - - + +
260B ARG* 1.3 71.0 - - - +
262B ILE* 1.3 62.1 + - - +
263B ILE* 4.1 22.1 + - + -
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B THR* 4.7 4.7 - - + -
229B LEU 3.4 7.9 - - - +
230B SER* 3.6 11.9 - - - +
253B HIS 3.9 0.2 - - - +
254B ILE* 3.3 7.3 - - - +
255B HIS* 2.8 67.4 + - + +
257B GLU* 4.3 10.5 - - + +
260B ARG* 3.4 48.7 - - + +
261B LEU* 1.3 76.3 - - - +
263B ILE* 1.3 67.3 + - - +
264B GLU* 3.8 25.6 - - + -
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Residues in contact with ILE 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B ILE* 4.6 2.0 - - + -
202B LEU* 4.6 11.2 - - + -
227B TYR* 4.2 17.7 - - + -
228B THR* 3.2 6.5 - - - +
229B LEU* 2.8 64.5 + - + +
246B ILE* 4.7 1.8 - - + -
250B LEU* 4.1 23.6 - - + -
252B ALA* 3.9 23.8 - - + -
253B HIS 3.5 2.2 - - - -
254B ILE* 4.0 18.8 - - + -
261B LEU* 4.4 19.7 - - + -
262B ILE* 1.3 77.6 - - - +
264B GLU* 1.3 63.9 + - - +
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Residues in contact with GLU 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B TYR 4.2 2.5 - - - -
228B THR* 3.8 16.5 - - + +
252B ALA* 3.3 2.4 - - - +
253B HIS* 2.7 49.3 + - + +
255B HIS* 3.1 30.6 + - - -
262B ILE* 3.8 13.9 - - + +
263B ILE* 1.3 77.8 - - - +
265B ASP* 1.3 73.0 + - - +
266B GLY 3.1 4.0 + - - -
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Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B LEU* 3.9 17.7 - - + +
227B TYR 3.4 7.9 + - - -
228B THR* 4.5 2.9 + - - -
251B ASN 3.8 12.5 - - - +
252B ALA* 4.2 1.1 - - - -
253B HIS* 4.0 28.6 + - + +
264B GLU* 1.3 80.6 - - - +
266B GLY* 1.3 65.5 + - - +
267B THR* 4.5 2.6 - - - +
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Residues in contact with GLY 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B LEU* 3.2 10.2 - - - +
227B TYR* 3.0 53.6 + - - -
250B LEU 4.9 1.1 - - - -
251B ASN 4.6 1.3 - - - -
252B ALA* 3.8 15.0 - - - -
264B GLU 3.1 4.6 - - - -
265B ASP* 1.3 82.6 - - - +
267B THR* 1.3 58.5 + - - -
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Residues in contact with THR 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B GLU* 4.2 22.5 + - + +
225B TYR 3.3 8.5 - - - +
226B LEU* 3.7 22.7 - - + -
227B TYR* 3.4 9.6 + - - -
250B LEU* 4.7 12.5 + - - +
251B ASN* 5.1 5.6 + - - +
265B ASP 3.9 3.3 + - - +
266B GLY* 1.3 78.2 - - - +
268B ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B LEU* 3.9 22.2 - - + +
218B LEU* 4.2 5.4 - - + -
224B GLU* 3.3 11.7 + - - +
225B TYR* 2.8 50.8 + - + +
227B TYR* 4.2 15.7 - - + -
267B THR* 1.3 75.3 - - - +
269B SER* 1.3 70.6 + - - +
272B ARG* 3.5 47.8 - - + +
273B LEU* 4.0 28.9 - - + +
276B VAL* 5.3 3.1 - - + -
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Residues in contact with SER 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ARG* 6.3 0.2 - - - -
223B ASN 3.8 3.8 - - - -
224B GLU* 3.8 12.3 + - - -
225B TYR* 5.4 0.4 - - - -
268B ILE* 1.3 79.2 - - - +
270B ALA* 1.3 53.8 + - - +
271B GLU* 3.3 19.7 - - - +
272B ARG* 3.1 25.9 + - - +
273B LEU* 2.8 35.1 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il